Genetic analysis of seedling root traits reveals the association of root trait with other agronomic traits in maize

Genetic control of root morphology in response to nitrogen across rapeseed diversity

Rapeseed (Brassica napus L.) is an oil-containing crop of great economic value but with considerable nitrogen requirement. Breeding root systems that efficiently absorb nitrogen from the soil could be a driver to ensure genetic gains for more sustainable rapeseed production. The aim of this study is to identify genomic regions that regulate root morphology in response to nitrate availability. The natural variability offered by 300 inbred lines was screened at two experimental locations. Seedlings grew hydroponically with low or elevated nitrate levels. Fifteen traits related to biomass production and root morphology were measured. On average across the panel, a low nitrate level increased the root-to-shoot biomass ratio and the lateral root length. A large phenotypic variation was observed, along with important heritability values and genotypic effects, but low genotype-by-nitrogen interactions. Genome-wide association study and bulk segregant analysis were used to identify loci regulating phenotypic traits. The first approach nominated 319 SNPs that were combined into 80 QTLs. Three QTLs identified on the A07 and C07 chromosomes were stable across nitrate levels and/or experimental locations. The second approach involved genotyping two groups of individuals from an experimental F2 population created by crossing two accessions with contrasting lateral root lengths. These individuals were found in the tails of the phenotypic distribution. Co-localized QTLs found in both mapping approaches covered a chromosomal region on the A06 chromosome. The QTL regions contained some genes putatively involved in root organogenesis and represent selection targets for redesigning the root morphology of rapeseed.

Identification of Quantitative Trait Loci Controlling Root Morphological Traits in an Interspecific Soybean Population Using 2D Imagery Data

Roots are the hidden and most important part of plants. They serve as stabilizers and channels for uptaking water and nutrients and play a crucial role in the growth and development of plants. Here, two-dimensional image data were used to identify quantitative trait loci (QTL) controlling root traits in an interspecific mapping population derived from a cross between wild soybean 'PI366121' and cultivar 'Williams 82'. A total of 2830 single-nucleotide polymorphisms were used for genotyping, constructing genetic linkage maps, and analyzing QTLs. Forty-two QTLs were identified on twelve chromosomes, twelve of which were identified as major QTLs, with a phenotypic variation range of 36.12% to 39.11% and a logarithm of odds value range of 12.01 to 17.35. Two significant QTL regions for the average diameter, root volume, and link average diameter root traits were detected on chromosomes 3 and 13, and both wild and cultivated soybeans contributed positive alleles. Six candidate genes, Glyma.03G027500 (transketolase/glycoaldehyde transferase), Glyma.03G014500 (dehydrogenases), Glyma.13G341500 (leucine-rich repeat receptor-like protein kinase), Glyma.13G341400 (AGC kinase family protein), Glyma.13G331900 (60S ribosomal protein), and Glyma.13G333100 (aquaporin transporter) showed higher expression in root tissues based on publicly available transcriptome data. These results will help breeders improve soybean genetic components and enhance soybean root morphological traits using desirable alleles from wild soybeans.

Early selection for drought tolerance in popcorn based on gene effects estimated in seedlings

Low rainfall rates are becoming increasingly frequent because of climate change, causing droughts and threatening world food security. For popcorn, drought is the most limiting abiotic factor for plant's growth and development. Thus, the water deficit directly impacts for crop productivity. Based on knowledge of the genetic basis of traits involved in stages of popcorn germination and seedling development under water stress, genotypes with potential for adaptation to adverse growing conditions can be selected early. Therefore, data on genetic effects and combining ability of 10 popcorn parents were compiled to propose breeding strategies for the development of cultivars with greater adaptation to water stress in the early stages. Forty-five diallel hybrids were evaluated under two different water regimes, that is, water stress and full irrigation. This corresponded to a water retention capacity of 25% and 70% of the germination paper. The plants were watered daily as needed for seven days. A range of factors were evaluated, that is, germination traits including the germination speed index and germination on the seventh day; shoot traits including length and dry weight; and root system including length, dry weight, root-to-shoot ratio, maximum root number, root network area, specific and root network length, and root volume. Breeding for drought adaption in the early stages of popcorn development can be successful when hybrids are used, because of the genetic effects of dominance (ϕ_s). These control the traits evaluated at the seedling stage. The combinations L61 x P2 and L71 x P3 were recommended, in view of the more successful performance estimated for traits related to the shoot and root system.

Genome-Wide Meta-Analysis of QTLs Associated with Root Traits and Implications for Maize Breeding

Root system architecture (RSA), also known as root morphology, is critical in plant acquisition of soil resources, plant growth, and yield formation. Many QTLs associated with RSA or root traits in maize have been identified using several bi-parental populations, particularly in response to various environmental factors. In the present study, a meta-analysis of QTLs associated with root traits was performed in maize using 917 QTLs retrieved from 43 mapping studies published from 1998 to 2020. A total of 631 QTLs were projected onto a consensus map involving 19,714 markers, which led to the prediction of 68 meta-QTLs (MQTLs). Among these 68 MQTLs, 36 MQTLs were validated with the marker-trait associations available from previous genome-wide association studies for root traits. The use of comparative genomics approaches revealed several gene models conserved among the maize, sorghum, and rice genomes. Among the conserved genomic regions, the ortho-MQTL analysis uncovered 20 maize MQTLs syntenic to 27 rice MQTLs for root traits. Functional analysis of some high-confidence MQTL regions revealed 442 gene models, which were then subjected to in silico expression analysis, yielding 235 gene models with significant expression in various tissues. Furthermore, 16 known genes viz., DXS2, PHT, RTP1, TUA4, YUC3, YUC6, RTCS1, NSA1, EIN2, NHX1, CPPS4, BIGE1, RCP1, SKUS13, YUC5, and AW330564 associated with various root traits were present within or near the MQTL regions. These results could aid in QTL cloning and pyramiding in developing new maize varieties with specific root architecture for proper plant growth and development under optimum and abiotic stress conditions.

Positional cloning and characterization reveal the role of a miRNA precursor gene ZmLRT in the regulation of lateral root number and drought tolerance in maize

Lateral roots play essential roles in drought tolerance in maize (Zea mays L.). However, the genetic basis for the variation in the number of lateral roots in maize remains elusive. Here, we identified a major quantitative trait locus (QTL), qLRT5-1, controlling lateral root number using a recombinant inbred population from a cross between the maize lines Zong3 (with many lateral roots) and 87-1 (with few lateral roots). Fine-mapping and functional analysis determined that the candidate gene for qLRT5-1, ZmLRT, expresses the primary transcript for the microRNA miR166a. ZmLRT was highly expressed in root tips and lateral root primordia, and knockout and overexpression of ZmLRT increased and decreased lateral root number, respectively. Compared with 87-1, the ZmLRT gene model of Zong3 lacked the second and third exons and contained a 14 bp deletion at the junction between the first exon and intron, which altered the splicing site. In addition, ZmLRT expression was significantly lower in Zong3 than in 87-1, which might be attributed to the insertions of a transposon and over large DNA fragments in the Zong3 ZmLRT promoter region. These mutations decreased the abundance of mature miR166a in Zong3, resulting in increased lateral roots at the seedling stage. Furthermore, miR166a post-transcriptionally repressed five development-related class-III homeodomain-leucine zipper genes. Moreover, knockout of ZmLRT enhanced drought tolerance of maize seedlings. Our study furthers our understanding of the genetic basis of lateral root number variation in maize and highlights ZmLRT as a target for improving drought tolerance in maize.

Overdominant expression of genes plays a key role in root growth of tobacco hybrids

Heterosis has greatly improved the yield and quality of crops. However, previous studies often focused on improving the yield and quality of the shoot system, while research on the root system was neglected. We determined the root numbers of 12 F₁ hybrids, all of which showed strong heterosis, indicating that tobacco F₁ hybrids have general heterosis. To understand its molecular mechanism, we selected two hybrids with strong heterosis, GJ (G70 × Jiucaiping No.2) and KJ (K326 × Jiucaiping No.2), and their parents for transcriptome analysis. There were 84.22% and 90.25% of the differentially expressed genes were overdominantly expressed. The enrichment analysis of these overdominantly expressed genes showed that "Plant hormone signal transduction", "Phenylpropanoid biosynthesis", "MAPK signaling pathway - plant", and "Starch and sucrose metabolism" pathways were associated with root development. We focused on the analysis of the biosynthetic pathways of auxin(AUX), cytokinins(CTK), abscisic acid(ABA), ethylene(ET), and salicylic acid(SA), suggesting that overdominant expression of these hormone signaling pathway genes may enhance root development in hybrids. In addition, Nitab4.5_0011528g0020、Nitab4.5_0003282g0020、Nitab4.5_0004384g0070 may be the genes involved in root growth. Genome-wide comparative transcriptome analysis enhanced our understanding of the regulatory network of tobacco root development and provided new ideas for studying the molecular mechanisms of tobacco root development.

Identification of Zinc Efficiency-Associated Loci (ZEALs) and Candidate Genes for Zn Deficiency Tolerance of Two Recombination Inbred Line Populations in Maize

Zinc (Zn) deficiency is one of the most common micronutrient disorders in cereal plants, greatly impairing crop productivity and nutritional quality. Identifying the genes associated with Zn deficiency tolerance is the basis for understanding the genetic mechanism conferring tolerance. In this study, the K22×BY815 and DAN340×K22 recombination inbred line (RIL) populations, which were derived from Zn-inefficient and Zn-efficient inbred lines, were utilized to detect the quantitative trait loci (QTLs) associated with Zn deficiency tolerance and to further identify candidate genes within these loci. The BLUP (Best Linear Unbiased Prediction) values under Zn-deficient condition (-Zn) and the ratios of the BLUP values under Zn deficient condition to the BLUP values under Zn-sufficient condition (-Zn/CK) were used to perform linkage mapping. In QTL analysis, 21 QTLs and 33 QTLs controlling the Zn score, plant height, shoot and root dry weight, and root-to-shoot ratio were detected in the K22×BY815 population and the DAN340×K22 population, explaining 5.5–16.6% and 4.2–23.3% of phenotypic variation, respectively. In addition, seventeen candidate genes associated with the mechanisms underlying Zn deficiency tolerance were identified in QTL colocalizations or the single loci, including the genes involved in the uptake, transport, and redistribution of Zn (ZmIRT1, ZmHMAs, ZmNRAMP6, ZmVIT, ZmNAS3, ZmDMAS1, ZmTOM3), and the genes participating in the auxin and ethylene signal pathways (ZmAFBs, ZmIAA17, ZmETR, ZmEIN2, ZmEIN3, ZmCTR3, ZmEBF1). Our findings will broaden the understanding of the genetic structure of the tolerance to Zn deficiency in maize.

Pinpointing genomic regions associated with root system architecture in rice through an integrative meta-analysis approach

Applying an integrated meta-analysis approach led to identification of meta-QTLs/ candidate genes associated with rice root system architecture, which can be used in MQTL-assisted breeding/ genetic engineering of root traits. Root system architecture (RSA) is an important factor for facilitating water and nutrient uptake from deep soils and adaptation to drought stress conditions. In the present research, an integrated meta-analysis approach was employed to find candidate genes and genomic regions involved in rice RSA traits. A whole-genome meta-analysis was performed for 425 initial QTLs reported in 34 independent experiments controlling RSA traits under control and drought stress conditions in the previous twenty years. Sixty-four consensus meta-QTLs (MQTLs) were detected, unevenly distributed on twelve rice chromosomes. The confidence interval (CI) of the identified MQTLs was obtained as 0.11-14.23 cM with an average of 3.79 cM, which was 3.88 times narrower than the mean CI of the original QTLs. Interestingly, 52 MQTLs were co-located with SNP peak positions reported in rice genome-wide association studies (GWAS) for root morphological traits. The genes located in these RSA-related MQTLs were detected and explored to find the drought-responsive genes in the rice root based on the RNA-seq and microarray data. Multiple RSA and drought tolerance-associated genes were found in the MQTLs including the genes involved in auxin biosynthesis or signaling (e.g. YUCCA, WOX, AUX/IAA, ARF), root angle (DRO1-related genes), lateral root development (e.g. DSR, WRKY), root diameter (e.g. OsNAC5), plant cell wall (e.g. EXPA), and lignification (e.g. C4H, PAL, PRX and CAD). The genes located within both the SNP peak positions and the QTL-overview peaks for RSA are suggested as novel candidate genes for further functional analysis. The promising candidate genes and MQTLs can be used as basis for genetic engineering and MQTL-assisted breeding of root phenotypes to improve yield potential, stability and performance in a water-stressed environment.

Genetic Variation for Traits Related to Phosphorus Use Efficiency in Lens Species at the Seedling Stage

Phosphorus (P) is an essential, non-renewable resource critical for crop productivity across the world. P is immobile in nature and, therefore, the identification of novel genotypes with efficient P uptake and utilization under a low P environment is extremely important. This study was designed to characterize eighty genotypes of different Lens species for shoot and root traits at two contrasting levels of P. A significant reduction in primary root length (PRL), total surface area (TSA), total root tips (TRT), root forks (RF), total dry weight (TDW), root dry weight (RDW) and shoot dry weight (SDW) in response to P deficiency was recorded. A principal component analysis revealed that the TDW, SDW and RDW were significantly correlated to P uptake and utilization efficiency in lentils. Based on total dry weight (TDW) under low P, L4727, EC718309, EC714238, PL-97, EC718348, DPL15, PL06 and EC718332 were found promising. The characterization of different Lens species revealed species-specific variations for the studied traits. Cultivated lentils exhibited higher P uptake and utilization efficiency as compared to the wild forms. The study, based on four different techniques, identified EC714238 as the most P use-efficient genotype. The genotypes identified in this study can be utilized for developing mapping populations and deciphering the genetics for breeding lentil varieties suited for low P environments.

Identification and Analysis of Zinc Efficiency-Associated Loci in Maize

Zinc (Zn) deficiency, a globally predominant micronutrient disorder in crops and humans, reduces crop yields and adversely impacts human health. Despite numerous studies on the physiological mechanisms underlying Zn deficiency tolerance, its genetic basis of molecular mechanism is still poorly understood. Thus, the Zn efficiency of 20 maize inbred lines was evaluated, and a quantitative trait locus (QTL) analysis was performed in the recombination inbred line population derived from the most Zn-efficient (Ye478) and Zn-inefficient inbred line (Wu312) to identify the candidate genes associated with Zn deficiency tolerance. On this basis, we analyzed the expression of ZmZIP1-ZmZIP8. Thirteen QTLs for the traits associated with Zn deficiency tolerance were detected, explaining 7.6-63.5% of the phenotypic variation. The genes responsible for Zn uptake and transport across membranes (ZmZIP3, ZmHMA3, ZmHMA4) were identified, which probably form a sophisticated network to regulate the uptake, translocation, and redistribution of Zn. Additionally, we identified the genes involved in the indole-3-acetic acid (IAA) biosynthesis (ZmIGPS) and auxin-dependent gene regulation (ZmIAA). Notably, a high upregulation of ZmZIP3 was found in the Zn-deficient root of Ye478, but not in that of Wu312. Additionally, ZmZIP4, ZmZIP5, and ZmZIP7 were up-regulated in the Zn-deficient roots of Ye478 and Wu312. Our findings provide a new insight into the genetic basis of Zn deficiency tolerance.

Overdominance at the Gene Expression Level Plays a Critical Role in the Hybrid Root Growth of Brassica napus

Despite heterosis contributing to genetic improvements in crops, root growth heterosis in rapeseed plants is poorly understood at the molecular level. The current study was performed to discover key differentially expressed genes (DEGs) related to heterosis in two hybrids with contrasting root growth performance (FO; high hybrid and FV; low hybrid) based on analysis of the root heterosis effect. Based on comparative transcriptomic analysis, we believe that the overdominance at the gene expression level plays a critical role in hybrid roots’ early biomass heterosis. Our findings imply that a considerable increase in up-regulation of gene expression underpins heterosis. In the FO hybrid, high expression of DEGs overdominant in the starch/sucrose and galactose metabolic pathways revealed a link between hybrid vigor and root growth. DEGs linked to auxin, cytokinin, brassinosteroids, ethylene, and abscisic acid were also specified, showing that these hormones may enhance mechanisms of root growth and the development in the FO hybrid. Moreover, transcription factors such as MYB, ERF, bHLH, NAC, bZIP, and WRKY are thought to control downstream genes involved in root growth. Overall, this is the first study to provide a better understanding related to the regulation of the molecular mechanism of heterosis, which assists in rapeseed growth and yield improvement.

Genome-wide association screening and verification of potential genes associated with root architectural traits in maize (Zea mays L.) at multiple seedling stages

Background

Breeding for new maize varieties with propitious root systems has tremendous potential in improving water and nutrients use efficiency and plant adaptation under suboptimal conditions. To date, most of the previously detected root-related trait genes in maize were new without functional verification. In this study, seven seedling root architectural traits were examined at three developmental stages in a recombinant inbred line population (RIL) of 179 RILs and a genome-wide association study (GWAS) panel of 80 elite inbred maize lines through quantitative trait loci (QTL) mapping and genome-wide association study.

Results

Using inclusive composite interval mapping, 8 QTLs accounting for 6.44–8.83 % of the phenotypic variation in root traits, were detected on chromosomes 1 (qRDW_v3-1-1 and qRDW/SDW_v3-1-1), 2 (qRBN_v1-2-1), 4 (qSUA_v1-4-1, qSUA_v2-4-1, and qROV_v2-4-1), and 10 (qTRL_v1-10-1, qRBN_v1-10-1). GWAS analysis involved three models (EMMAX, FarmCPU, and MLM) for a set of 1,490,007 high-quality single nucleotide polymorphisms (SNPs) obtained via whole genome next-generation sequencing (NGS). Overall, 53 significant SNPs with a phenotypic contribution rate ranging from 5.10 to 30.2 % and spread all over the ten maize chromosomes exhibited associations with the seven root traits. 17 SNPs were repeatedly detected from at least two growth stages, with several SNPs associated with multiple traits stably identified at all evaluated stages. Within the average linkage disequilibrium (LD) distance of 5.2 kb for the significant SNPs, 46 candidate genes harboring substantial SNPs were identified. Five potential genes viz. Zm00001d038676, Zm00001d015379, Zm00001d018496, Zm00001d050783, and Zm00001d017751 were verified for expression levels using maize accessions with extreme root branching differences from the GWAS panel and the RIL population. The results showed significantly (P < 0.001) different expression levels between the outer materials in both panels and at all considered growth stages.

Conclusions

This study provides a key reference for uncovering the complex genetic mechanism of root development and genetic enhancement of maize root system architecture, thus supporting the breeding of high-yielding maize varieties with propitious root systems.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07874-x.

Primary Root and Mesocotyl Elongation in Maize Seedlings: Two Organs with Antagonistic Growth below the Soil Surface

Maize illustrates one of the most complex cases of embryogenesis in higher plants that results in the development of early embryo with distinctive organs such as the mesocotyl, seminal and primary roots, coleoptile, and plumule. After seed germination, the elongation of root and mesocotyl follows opposite directions in response to specific tropisms (positive and negative gravitropism and hydrotropism). Tropisms represent the differential growth of an organ directed toward several stimuli. Although the life cycle of roots and mesocotyl takes place in darkness, their growth and functions are controlled by different mechanisms. Roots ramify through the soil following the direction of the gravity vector, spreading their tips into new territories looking for water; when water availability is low, the root hydrotropic response is triggered toward the zone with higher moisture. Nonetheless, there is a high range of hydrotropic curvatures (angles) in maize. The processes that control root hydrotropism and mesocotyl elongation remain unclear; however, they are influenced by genetic and environmental cues to guide their growth for optimizing early seedling vigor. Roots and mesocotyls are crucial for the establishment, growth, and development of the plant since both help to forage water in the soil. Mesocotyl elongation is associated with an ancient agriculture practice known as deep planting. This tradition takes advantage of residual soil humidity and continues to be used in semiarid regions of Mexico and USA. Due to the genetic diversity of maize, some lines have developed long mesocotyls capable of deep planting while others are unable to do it. Hence, the genetic and phenetic interaction of maize lines with a robust hydrotropic response and higher mesocotyl elongation in response to water scarcity in time of global heating might be used for developing more resilient maize plants.

Root Growth Adaptation to Climate Change in Crops

Climate change is threatening crop productivity worldwide and new solutions to adapt crops to these environmental changes are urgently needed. Elevated temperatures driven by climate change affect developmental and physiological plant processes that, ultimately, impact on crop yield and quality. Plant roots are responsible for water and nutrients uptake, but changes in soil temperatures alters this process limiting crop growth. With the predicted variable climatic forecast, the development of an efficient root system better adapted to changing soil and environmental conditions is crucial for enhancing crop productivity. Root traits associated with improved adaptation to rising temperatures are increasingly being analyzed to obtain more suitable crop varieties. In this review, we will summarize the current knowledge about the effect of increasing temperatures on root growth and their impact on crop yield. First, we will describe the main alterations in root architecture that different crops undergo in response to warmer soils. Then, we will outline the main coordinated physiological and metabolic changes taking place in roots and aerial parts that modulate the global response of the plant to increased temperatures. We will discuss on some of the main regulatory mechanisms controlling root adaptation to warmer soils, including the activation of heat and oxidative pathways to prevent damage of root cells and disruption of root growth; the interplay between hormonal regulatory pathways and the global changes on gene expression and protein homeostasis. We will also consider that in the field, increasing temperatures are usually associated with other abiotic and biotic stresses such as drought, salinity, nutrient deficiencies, and pathogen infections. We will present recent advances on how the root system is able to integrate and respond to complex and different stimuli in order to adapt to an increasingly changing environment. Finally, we will discuss the new prospects and challenges in this field as well as the more promising pathways for future research.

The search for yield predictors for mature field-grown plants from juvenile pot-grown cassava (Manihot esculenta Crantz)

Cassava is the 6th most important source of dietary energy in the world but its root system architecture (RSA) had seldom been quantified. Ability to select superior genotypes at juvenile stages can significantly reduce the cost and time for breeding to bridge the large yield gap. This study adopted a simple approach to phenotyping RSA traits of juvenile and mature cassava plants to identify genotypic differences and the relationships between juvenile traits and harvest index of mature plants. Root classes were categorised and root and shoot traits of eight (8) juvenile pot-grown cassava genotypes, were measured at 30 and 45 days after planting (DAP). The same or related traits were measured at 7 months after planting of the same genotypes grown in the field while yield and yield components were measured in 12-months old field-grown plants. The field experiment was done in 2017 and repeated in 2018. Differences between genotypes for the measured traits were explored using analysis of variance (ANOVA) while traits in juvenile plants were correlated or regressed onto traits measured in 7- and 12-months old plants. The results show significant genotypic variations for most of the traits measured in both juvenile and 7-months old plants. In the 12-months old plants, differences between genotypes were consistent for both 2017 and 2018. Broad-sense heritability was highest for the number of commercial roots (0.87) and shoot fresh weight (0.78) and intermediate for the total number of roots (0.60), harvest index (0.58), fresh weight of roots (0.45). For all the sampling time points or growth stages, there were greater correlations between traits measured at a particular growth stage than between the same traits at different growth stages. However, some juvenile-mature plant trait relationships were significant, positive and consistent for both 2017 and 2018. For example, total root length and the total number of roots in 30 DAP, and branching density of upper nodal roots in 45 DAP, positively correlated with harvest index of 12-months old plants in both 2017 and 2018. Similarly, the diameter of nodal roots, for example, had a negative, significant correlation with fresh shoot biomass of mature plants in both 2017 and 2018. Regression of traits measured in 30 DAP explained up to 22% and 36% of the variation in HI of mature plants in 2017 and 2018, respectively. It is concluded that the simple, rapid, inexpensive phenotyping approach adopted in this study is robust for identifying genotypic variations in juvenile cassava using root system traits. Also, the results provide seminal evidence for the existence of useful relationships between traits of juvenile and mature cassava plants that can be explored to predict yield and yield components.

Identification of Quantitative Trait Loci Controlling Ethylene Production in Germinating Seeds in Maize (Zea mays L.)

Plant seed germination is a crucial developmental event that has significant effects on seedling establishment and yield production. This process is controlled by multiple intrinsic signals, particularly phytohormones. The gaseous hormone ethylene stimulates seed germination; however, the genetic basis of ethylene production in maize during seed germination remains poorly understood. In this study, we quantified the diversity of germination among 14 inbred lines representing the parental materials corresponding to multiple recombinant inbred line (RIL) mapping populations. Quantitative trait loci (QTLs) controlling ethylene production were then identified in germinating seeds from an RIL population constructed from two parental lines showing differences in both germination speed and ethylene production during germination. To explore the possible genetic correlations of ethylene production with other traits, seed germination and seed weight were evaluated using the same batch of samples. On the basis of high-density single nucleotide polymorphism-based genetic linkage maps, we detected three QTLs for ethylene production in germinating seeds, three QTLs for seed germination, and four QTLs for seed weight, with each QTL explaining 5.8%–13.2% of the phenotypic variation of the trait. No QTLs were observed to be co-localized, suggesting that the genetic bases underlying the three traits are largely different. Our findings reveal three chromosomal regions responsible for ethylene production during seed germination, and provide a valuable reference for the future investigation of the genetic mechanism underlying the role of the stress hormone ethylene in maize germination control under unfavourable external conditions.

Root diversity in sesame (Sesamum indicum L.): insights into the morphological, anatomical and gene expression profiles

Sesame harbors a large diversity in root morphological and anatomical traits and a high root biomass improves the plant aboveground biomass as well as the seed yield. Sesame provides one of the most nutritious and healthy vegetable oils, sparking an increasing demand of its seeds. However, with the low yield and productivity of sesame, there is still a huge gap between the seed demand and supply. Improving the root system has a high potential to increase crop productivity, but information on the diversity of the sesame root systems is still lacking. In this study, 40 diverse sesame varieties were grown in soil and hydroponics systems and the diversity of the root system was investigated. The results showed that sesame holds a large root morphological and anatomical diversity, which can be harnessed in breeding programmes. Based on the clustering of the genotypes in hydroponics and soil culture systems, we found that similar genotypes were commonly clustered either in the small-root or in the big-root group, indicating that the hydroponics system can be employed for a large-scale root phenotyping. Our results further revealed that the root biomass positively contributes to increased seed yield in sesame, based on multi-environmental trials. By comparing the root transcriptome of two contrasting genotypes, 2897 differentially expressed genes were detected and they were enriched in phenylpropanoid biosynthesis, starch and sucrose metabolism, stilbenoid, diarylheptanoid and gingerol biosynthesis, flavonoid biosynthesis, suggesting that these pathways are crucial for sesame root growth and development. Overall, this study sheds light on the diversity of sesame root system and offers the basis for improving root traits and increasing sesame seed yield.

Salinity Stress Alters Root Morphology and Root Hair Traits in Brassica napus

Plant roots show morphological plasticity and play a substantial role in tolerance to various edaphic stresses. The aim of this study was to explore salinity-induced morphogenic responses of root traits and root hairs of two rapeseed varieties, BARI Sarisha-8 and Binasarisha-5, at the reproductive stage and perceive the effects on their reproductive growth. The experiment was conducted in a hydroponic culture. Two treatments, 0 mM NaCl as control and 100 mM NaCl, were imposed 55 d after germination. Plants exposed to 100 mM NaCl for seven days displayed greater damage in the leaves, flowers, and siliquae compared to control. Length of root hairs on first-order and third-order lateral roots, density of root hairs on first-order lateral roots, and length of third-order lateral roots were significantly greater by 91%, 22%, 29%, and 48%, respectively, in the treated condition compared to the control. An increase in estimated root surface area by 20% under salt stress conditions indicated that the spontaneous responses of plants to uptake more water and nutrients allowed a plant to cope with stressful conditions. The results of this study suggest that any future stress breeding programs should consider plasticity of root traits intensively.